README.md

Bran

This repository is named after Bran Stark from Game of Thrones, who used his Greensight ability to discover Jon Snow's Targaryen ancestry. This tool builds a family tree from data exported from Transnetyx.

Installation

Install the following packages in R:

install.packages('kinship2')
install.packages('plyr')
install.packages('dplyr')
install.packages('wrapr')
install.packages("readxl")
install.packages("RColorBrewer")
install.packages("optparse")

Getting Started

1. Test that this repository runs. Use the included file sample_ped_tab.csv:

   Rscript R/plot_family_tree.R -i data/sample_ped_tab.csv -p 1

2. Plot the family tree. Use the "Export to Excel" function in the Dashboard/Mouse section of Transnetyx to obtain a My_Mice.xlsx file. Move it into data, then run the same script as above.

   Rscript R/plot_family_tree.R -i data/My_Mice.xlsx

   This outputs two files, the pedegree into figures and a cleaned up csv file into data/troubleshooting. Open the cleaned up csv file, then update it with genotyping information and colors.

3. Merge your annotated file with new data. In the future, when you download a new My_Mice.xlsx file, to bring in your annotations from you old file, run the following script:

   Rscript R/weave_data.R -i data/initial_data.csv -n data/My_Mice.xlsx

Data Requirements

At minimum, your exported data needs the following columns: Sex, Mouse ID, Father ID, and Mother ID. The rest of the columns are optional. If you include the DOD column, the 'alive' field will automatically be computed for you.

I recommend setting a default view with the following columns: Use, Strain, Sex, Age, DOB, DOD, Mouse ID, Genotype, Labels, Cage ID, Notes, SystemId, Father ID, Mother ID, Rack, Position.

Contributing

Please create a Github issue or reach out to me directly.

Copyright

This code is copyright by Harrison Wang in 2023.